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DNA nanotechnology leverages the molecular design resolution of the DNA double helix to fold and tile matter into designer architectures. Recent advances in bioinorganic chemistry have exploited the affinity of soft nucleobase functional groups for silver ions in order to template the growth of silver nanoclusters by templated reduction. The coupling of the spatial resolution of DNA nanotechnology and the atomic precision of DNA-based nanocluster synthesis has not been realized. Here we develop a method using 3D DNA crystals to employ silver-ion-mediated base pairs as nucleation sites for atomically-precise nanocluster growth. By leveraging the topology of DNA tensegrity triangles, we provide a mesoporous 3D lattice that is robust to reducing conditions, enabling precise spatial templating. Use of in situ confocal fluorescence microscopy allows for the direct observation of reaction kinetics and reconstruction of the optical bandgap. Control over reaction time and stoichiometry, base pair identity, and buffer composition enable precise tuning of the atomic composition and optical properties of the ensuing nanoclusters. The resulting crystals are of diffraction quality, yielding molecular structures of Ag4 and Ag6 in 3D. Inter-cluster distances of less than 2 nm show strong plasmonic coupling, with red shifting observed relative to literature standards. We anticipate that these results will yield advances in materials synthesis, DNA-based plasmonic crystals, and optically-active nanoelectronics.
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DNA Glass: Encasing Diffraction-Quality, Mesoporous DNA Crystals in Silica
Self-assembling DNA crystals have emerged over the last two decades as an efficient and effective means of organizing matter at the nanoscale, but functionalization of these lattices has proved challenging as physiological buffer conditions are required to maintain structural integrity. In this manuscript, we demonstrate the silicification of porous DNA crystals using sol-gel chemistry. We identify reaction conditions that produce the minimum coating thickness to confer environmental protection, and subsequently measure the protective ability of the silica coating to various stressors, including heat, low ionic strength solution, organic solvents, and unprotected flash freezing. By soaking ions and dyes into the lattice after silica coating, we demonstrate that the crystals maintain their pores, and that the major groove of the DNA can still be used as a site-specific template for chemical modifications. We image a library of different crystal motifs by electron microscopy and confirm the presence of silica using energy dispersive spectroscopy. Finally, we perform X-ray diffraction on these crystals, both with and without cryoprotection and determine the structure of the DNA frame, underscoring the conserved molecular order after coating. We anticipate these mesoporous silica composites for use in applications involving extreme, non-physiological conditions and for experiments which utilize the DNA glass described here as a template for surface science.
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- Award ID(s):
- 2317843
- PAR ID:
- 10626940
- Publisher / Repository:
- ACS
- Date Published:
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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- Free Publicly Accessible Full Text
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Accepted Manuscript
- Posted Content:
- https://doi.org/10.26434/chemrxiv-2025-ppztw
